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reflex_step0_dem_conditioning.py
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reflex_step0_dem_conditioning.py
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#!/usr/bin/env python
"""
REFlEx - Step0 - Hydrogical Conditioning
__date__ = '20230330'
__version__ = '2.1.0'
__author__ =
'Mauro Arcorace' (mauro.arcorace@cimafoundation.org',
'Andrea Libertino (andrea.libertino@cimafoundation.org'
__library__ = 'REFlEx'
General command line:
### python reflex_step0_dem_conditioning.py -log_file "/path/to/log.txt" -settings_file "settings.json" -dem "/path/to/dem.tif" -base_path "/path/to/base_folder" (-stream "/path/to/stream.shp")
Version(s):
20190220 (1.0.0) --> Beta release
20210126 (1.5.0) --> Official release
20220118 (1.6.0) --> Added simplified carving
20220406 (2.0.0) --> Full revision
20230330 (2.1.0) --> Simplify integration with local grass and proj installations
"""
# -------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------
# Import full libraries
import geopandas as gpd
from lib.reflex_tools_utils import Give_Elapsed_Time, Start_GRASS_py3, set_logging, read_file_json
import logging
from matplotlib import pyplot as plt
import numpy as np
import os
from osgeo import gdal, osr, gdalconst
from pysheds.grid import Grid
import rasterio
from rasterio.warp import calculate_default_transform, reproject, Resampling
import richdem as rd
from scipy import interpolate
from scipy.signal import savgol_filter
import shutil
import subprocess
import time, sys
from argparse import ArgumentParser
import json
# -------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------
# Algorithm information
alg_name = 'REFlEx - STEP 0 - Dem Conditioning'
alg_version = '2.1.0'
alg_release = '2023-03-30'
# Algorithm parameter(s)
time_format = '%Y%m%d%H%M'
# -------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------
# Script Main
def main():
# -------------------------------------------------------------------------------------
# Get algorithm settings
config_file, alg_log, input_dem_geotiff, input_stream_shapefile, base_path = get_args()
# Set algorithm settings
data_settings = read_file_json(config_file)
os.makedirs(os.path.dirname(alg_log), exist_ok=True)
set_logging(logger_file=alg_log)
overwrite_mode = True
quiet_mode = True
# -------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------
# Info algorithm
logging.info(' ============================================================================ ')
logging.info(' ================ REFlEx - Rapid Estimation od FLood EXtent ================= ')
logging.info(' ==> ' + alg_name + ' (Version: ' + alg_version + ' Release_Date: ' + alg_release + ')')
logging.info(' ==> START ... ')
logging.info(' ')
# -------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------
# GET PARAMETERS FROM CONFIG FILE
# -------------------------------
# Path to executable and version
script_ver = data_settings["algorithm"]["version"]
grass_bin = data_settings["algorithm"]["grass_bin"]
# Domain and DEM info
acp_x = data_settings["domain"]["name"].upper()
domain_name = data_settings["domain"]["name"]
rrs_km = data_settings["domain"]["res_km"]
in_res_DD = data_settings["domain"]["res_deg"]
rrs_m = rrs_km * 1000
rrs = data_settings["domain"]["res_str"]
source_epsg = data_settings["domain"]["source_epsg"]
target_epsg = data_settings["domain"]["target_epsg"]
min_threshold = data_settings["domain"]["min_nonnull_value"]
# Step settings
step0_dir_name = data_settings["step_0"]["dir_name"].replace("{base_path}", base_path)
# Preprocessing
remove_sinks_enabled = data_settings["step_0"]["preprocessing"]["hydrodem_remove_sink"]
epsilon_filling_enabled = data_settings["step_0"]["preprocessing"]["richdem_eps_filling"]
pysheds_preprocessing_enabled = data_settings["step_0"]["preprocessing"]["pysheds_pit_remove_and_solve_flats"]
# Stream burning
method_dem_burning = data_settings["step_0"]["stream_burning"]["burning_method"]
if method_dem_burning is None:
stream_burning_enabled = False
else:
stream_burning_enabled = True
try:
proj_lib = data_settings["algorithm"]["proj_db"]
except:
proj_lib = "/usr/share/proj"
carve_depth_m = data_settings["step_0"]["stream_burning"]["A"]["carve_depth_m"]
filtering_magnitude = data_settings["step_0"]["stream_burning"]["B"]["filtering_magnitude"]
buffer_distance_cells = data_settings["step_0"]["stream_burning"]["B"]["buffer_distance_cells"]
# -------------------------------------------------------------------------------------
# -------------------------------------------------------------------------------------
# CREATE OUTPUT DIRECTORIES
# -------------------------
# Define output MAIN directory
# out_folder='%s_%s_%s_%s'%(str(out_folder),str(buffer_cells),str(int(filtering_magnitude)),str(target_epsg))
main_output_dir = os.path.join(base_path, step0_dir_name)
logging.info('--> Output main directory: %s' % main_output_dir)
if not os.path.exists(main_output_dir):
os.makedirs(main_output_dir)
# Define output tmp sub-directory
out_tmp_dirname = 'tmp'
tmp_output_dir = os.path.join(main_output_dir, out_tmp_dirname)
logging.info('--> Output tmp sub-directory: %s' % tmp_output_dir)
if not os.path.exists(tmp_output_dir):
os.makedirs(tmp_output_dir)
# Define output tmp sub-directory
if method_dem_burning == 'B':
out_segment_dirname = 'segments'
out_segment_dir = os.path.join(main_output_dir, out_segment_dirname)
logging.info('--> Output segment sub-directory: %s' % out_segment_dir)
if not os.path.exists(out_segment_dir):
os.makedirs(out_segment_dir)
################################################################################
################################################################################
# CHECK EPSG CODE
# -------------------------
if target_epsg != source_epsg:
logging.info("Projecting raster to EPSG to %s..." % (str(target_epsg)))
output_DTM_file_prj = Project_geotiff(input_dem_geotiff, source_epsg, target_epsg, tmp_output_dir)
logging.info("Projecting vector from EPSG %s to %s..." % (str(source_epsg), str(target_epsg)))
output_prj_stream_shpfile = Project_shapefile(input_stream_shapefile, source_epsg, target_epsg, tmp_output_dir)
else:
logging.info("--> Not required to projecting input raster or vector files.")
output_DTM_file_prj = input_dem_geotiff
output_prj_stream_shpfile = input_stream_shapefile
################################################################################
################################################################################
# INITIALIZE GRASS
# ----------------
# Start GRASS
logging.info("--> Starting GRASS..")
os.environ['PROJ_LIB'] = proj_lib
if not os.path.join(proj_lib, "proj.db"):
logging.error(
" ERROR! proj.db file not found at " + proj_lib + " Please add the 'proj_db' key under the 'algorithm' key of the setting file to specify the location!")
raise FileNotFoundError
from grass_session import TmpSession
# Configure grass
os.environ['GISDBASE'] = os.path.join(step0_dir_name, "grass_temp", "")
os.environ['GRASSBIN'] = grass_bin
os.environ['GISBASE'] = os.popen(grass_bin + ' --config path').read().strip('\n')
gpydir = os.path.join(os.environ['GISBASE'], "etc", "python")
sys.path.append(gpydir)
# Import GRASS Python bindings
import grass.script as grass
import grass.script.setup as gsetup
from grass.pygrass.modules.shortcuts import general as g
from grass.pygrass.modules.shortcuts import raster as r
from grass.pygrass.modules.shortcuts import vector as v
from grass.pygrass.modules.shortcuts import database as db
from grass.pygrass.modules import Module
from grass.exceptions import GrassError
if os.path.isdir(os.path.join(os.environ['GISDBASE'])):
shutil.rmtree(os.path.join(os.environ['GISDBASE']))
with TmpSession(gisdb=os.environ['GISDBASE'], location="wgs84", create_opts='EPSG:4326'):
# Define alias for GRASS modules
r.out_gdal = Module('r.out.gdal')
try:
r.stream_basins = Module('r.stream.basins')
except GrassError:
logging.warning('r.stream.basins not found... INSTALL')
g.extension(extension='r.stream.basins', operation="add")
r.stream_basins = Module('r.stream.basins')
try:
r.stream_extract = Module('r.stream.extract')
except GrassError:
logging.warning('r.stream.extract not found... INSTALL')
g.extension(extension='r.stream.extract', operation="add")
r.stream_extract = Module('r.stream.extract')
try:
r.stream_distance = Module('r.stream.distance')
except GrassError:
logging.warning('r.stream.distance not found... INSTALL')
g.extension(extension='r.stream.distance', operation="add")
r.stream_distance = Module('r.stream.distance')
try:
r.stream_distance = Module('r.stream.order')
except GrassError:
logging.warning('r.stream.distance not found... INSTALL')
g.extension(extension='r.stream.order', operation="add")
r.stream_order = Module('r.stream.order')
r.grow_distance = Module('r.grow.distance')
r.to_vect = Module('r.to.vect')
v.to_db = Module('v.to.db')
v.db_dropcolumn = Module('v.db.dropcolumn')
v.db_addcolumn = Module('v.db.addcolumn')
v.what_rast = Module('v.what.rast')
v.out_ogr = Module('v.out.ogr')
v.db_renamecolum = Module('v.db.renamecolumn')
v.db_select = Module('v.db.select')
v.db_addtable = Module('v.db.addtable')
v.in_ogr = Module('v.in.ogr')
v.db_update = Module('v.db.update')
v.db_select = Module('v.db.select')
v.to_rast = Module('v.to.rast')
db.out_ogr = Module('db.out.ogr')
v.to_points_new = Module('v.to.points')
# ----------------
################################################################################
################################################################################
# DEFINE VARIABLE NAMES
# ---------------------
progress_dem = 'r_%s_%s_dem_in_progress' % (domain_name, str(rrs))
dem_coverage = 'r_%s_%s_dem_coverage' % (domain_name, str(rrs))
hydrodem_dem = 'r_%s_%s_dem_hydrodem' % (domain_name, str(rrs))
conditioned_dem = 'r_%s_%s_conddem' % (domain_name, rrs)
filled_dem = 'r_%s_%s_filled_dem' % (domain_name, rrs)
# ---------------------
code_start_time = time.time()
################################################################################
################################################################################
# IMPORT DEM INTO GRASS AND MAKE HILLSHADE
# ----------------------------------------
dem_processed = os.path.join(tmp_output_dir, progress_dem)
# Import DEM file into GRASS
r.external(input=output_DTM_file_prj, output='temp_in')
g.region(raster='temp_in')
r.mapcalc("raw_dem=if(temp_in<" + str(min_threshold) + ",null(),temp_in)", overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input="raw_dem", output=dem_processed, type="Float32", createopt="COMPRESS=DEFLATE", nodata=-9999, overwrite=overwrite_mode, quiet=quiet_mode)
############################
# Compute DEM coverage
r.mapcalc("%s=not(if(isnull(%s)))" % (dem_coverage, 'raw_dem'), overwrite=overwrite_mode, quiet=quiet_mode)
# ----------------------------------------
################################################################################
################################################################################
# FILTERING DEM
# -------------
# Smooth input DEM using mdenoise (http://carlosgrohmann.com/blog/denoise-srtm-grass/)
# /application/pi/Documents/Reflex_model/bin/mdenoise -i /application/pi/Documents/LIDAR/MATTM_LiDAR_MAGRA_resampled_bln_10m_3003_masked_trnslt.asc -o /application/pi/Documents/LIDAR/MATTM_LiDAR_MAGRA_resampled_bln_10m_3003_masked_trnslt_denoise5.asc -z -t 0.9 -n 5
# Removing sinks by executing hydrodem
if (remove_sinks_enabled is True):
logging.info('-> Removing sinks by executing hydrodem...')
r.hydrodem(flags='a', input='raw_dem', output=hydrodem_dem, mod='4', size='4', overwrite=overwrite_mode,
quiet=quiet_mode)
r.out_gdal(input=hydrodem_dem, output=dem_processed, createopt="COMPRESS=DEFLATE",
overwrite=overwrite_mode, quiet=quiet_mode)
else:
pass
# ------------------------------------------------------------------------------------------------------------------
# ------------------------------------------------------------------------------------------------------------------
# DEM preprocessing
# Compute RichDEM epsilon filling
if epsilon_filling_enabled:
# Read raw dem
input_E = rd.LoadGDAL(dem_processed, no_data=-9999)
logging.info('-> Converting numpy to richdem array...')
# DEM Epsilon filling
logging.info('-> Epsilon filling raw DEM...')
rd.FillDepressions(input_E, epsilon=True, in_place=True)
rd.SaveGDAL(dem_processed, input_E)
else:
pass
# Solve flats using pysheds
if pysheds_preprocessing_enabled:
logging.info('-> Pit filling and solving flats with pysheds...')
grid = Grid.from_raster('%s' % str(dem_processed))
dem = grid.read_raster('%s' % str(dem_processed), window=grid.bbox, window_crs=grid.crs)
dem.nodata = -9999
pit_filled_dem = grid.fill_pits(dem, nodata_out=np.nan)
inflated_dem = grid.resolve_flats(pit_filled_dem, nodata_out=np.nan)
grid.to_raster(inflated_dem, dem_processed, nodata=-9999, apply_output_mask=True)
else:
pass
out_dem_filled_file = '%s/%s.tif' % (main_output_dir, filled_dem)
gdal.Translate(out_dem_filled_file, dem_processed, format="GTiff", creationOptions=["COMPRESS=DEFLATE"], outputType=gdalconst.GDT_Float32)
# ------------------------------------------------------------------------------------------------------------------
# ------------------------------------------------------------------------------------------------------------------
# Import filtered DEM raster file and overwrite the raw dem
r.external(input=out_dem_filled_file, output='raw_dem', overwrite=overwrite_mode, quiet=quiet_mode)
g.region(raster='raw_dem')
r.mask(raster=dem_coverage)
# ------------------------------------------------------------------------------------------------------------------
# ------------------------------------------------------------------------------------------------------------------
# Stream burning
if stream_burning_enabled is True:
v.in_ogr(input=output_prj_stream_shpfile, output='streams_vect', quiet=quiet_mode)
if method_dem_burning == 'A':
logging.info('-> Simplified stream burning...')
v.to_rast(input='streams_vect', type='line', output='streams_rast', use='val', value=carve_depth_m,
quiet=quiet_mode)
r.mapcalc(expression="out_conditioned_dem=if(isnull(streams_rast),raw_dem,raw_dem-streams_rast)",
quiet=quiet_mode)
# Export and define output variable
r.out_gdal(input='out_conditioned_dem', output='%s/%s.tif' % (main_output_dir, conditioned_dem), type='Float32',
overwrite=overwrite_mode, nodata=-9999, createopt="COMPRESS=DEFLATE", quiet=quiet_mode)
# dem_input_cond_file='%s/%s.tif'%(main_output_dir,conditioned_dem)
out_dem_cond_file = '%s/%s.tif' % (main_output_dir, conditioned_dem)
logging.info('-> Simplified stream burning...DONE')
elif method_dem_burning == 'B':
# Get stream ID list
stream_ID_list_orig = []
p = grass.pipe_command('v.db.select', flags="c", map='streams_vect', columns='stream', quiet=quiet_mode)
for line in p.stdout:
stream_ID_list_orig.append(line.decode("utf-8").rstrip('\r\n'))
p.wait()
logging.info("--> stream_ID_list_orig: %s" % stream_ID_list_orig)
# Get stream ID level and depth list from input vector file
shape_input_stream_network = gpd.read_file(output_prj_stream_shpfile)
shape_input_stream_network_sorted = shape_input_stream_network.iloc[
shape_input_stream_network['stream'].sort_values(ascending=[True]).index.values]
stream_ID_array = shape_input_stream_network_sorted['stream'].values
stream_ID_level_array = shape_input_stream_network_sorted['Level'].values
stream_ID_outlet_depth_array = shape_input_stream_network_sorted['Depth'].values
stream_ID_inlet_depth_array = shape_input_stream_network_sorted['Depth_beg'].values
stream_ID_list = stream_ID_array.tolist()
stream_ID_level_list = stream_ID_level_array.tolist()
stream_ID_outlet_depth_list = stream_ID_outlet_depth_array.tolist()
stream_ID_inlet_depth_list = stream_ID_inlet_depth_array.tolist()
del shape_input_stream_network, shape_input_stream_network_sorted
# Extract maximum area value and identify location of sub-basin outlet for %s streams..
tot_streams = len(stream_ID_list)
logging.info(
"--> Burning streams into DEM for %s branches (this process might take several minutes).." % tot_streams)
logging.info("--> stream_ID_list: %s" % stream_ID_list)
logging.info("--> stream_ID_level_list: %s" % stream_ID_level_list)
logging.info("--> stream_ID_outlet_depth_list: %s" % stream_ID_outlet_depth_list)
logging.info("--> stream_ID_inlet_depth_list: %s" % stream_ID_inlet_depth_list)
segm_count = 0
# for ID in stream_ID_list:
for k in range(len(stream_ID_list)):
ID = str(stream_ID_list[k])
burning_level = int(stream_ID_level_list[k])
burning_depth = float(stream_ID_outlet_depth_list[k])
already_burned_depth = float(stream_ID_inlet_depth_list[k])
logging.info("--> Burning stream no.: %s" % ID)
logging.info("--> Burning stream no. %s with level %s and carve stream from %s to %s m of depth" % (
ID, str(burning_level), str(already_burned_depth), str(burning_depth)))
flat_burning_mode_flag = False
if already_burned_depth == burning_depth:
flat_burning_mode_flag = True
else:
pass
g.region(raster='raw_dem')
g.region(zoom='raw_dem')
v.extract(input='streams_vect', type='line', where='stream=%s' % (str(ID)),
output='stream_i_vect_%s' % str(ID), overwrite=overwrite_mode, quiet=quiet_mode)
v.out_ogr(input='stream_i_vect_%s' % str(ID),
output='%s/stream_i_vect_%s.gpkg' % (tmp_output_dir, str(ID)),
format="GPKG", type="line", overwrite=overwrite_mode, quiet=quiet_mode)
v.to_rast(input='stream_i_vect_%s' % str(ID), output='streams_rast_%s' % str(ID), type='line',
use='attr',
attribute_column='cat_', overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='streams_rast_%s' % str(ID), output='%s/streams_rast_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
r.mapcalc("stream_i_tmp_%s=if(streams_rast_%s==%s,%s,null())" % (str(ID), str(ID), str(ID), str(ID)),
overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='stream_i_tmp_%s' % str(ID), output='%s/stream_i_tmp_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
r.mapcalc("dem_nan_mask_i_%s=if(!isnull(raw_dem),1,0)" % (str(ID)), overwrite=overwrite_mode,
quiet=quiet_mode)
r.mapcalc("stream_i_%s=if(dem_nan_mask_i_%s==1,stream_i_tmp_%s,null())" % (str(ID), str(ID), str(ID)),
overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='stream_i_%s' % str(ID), output='%s/stream_i_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
in_region = grass.region()
logging.info("--> GRASS computational region: '%s'" % in_region)
try:
r.thin(input='stream_i_%s' % str(ID), output='stream_i_thinned_%s' % str(ID))
except:
print('SKIPPED stream_i_%s' % str(ID))
continue
r.out_gdal(input='stream_i_thinned_%s' % str(ID),
output='%s/stream_i_thinned_%s.tif' % (tmp_output_dir, ID), createopt="COMPRESS=DEFLATE",
overwrite=overwrite_mode, quiet=quiet_mode)
r.to_vect(input='stream_i_thinned_%s' % str(ID), output='stream_i_rst_vct_%s' % str(ID), type='line',
overwrite=overwrite_mode, quiet=quiet_mode)
v.out_ogr(input='stream_i_rst_vct_%s' % str(ID), type="line",
output='%s/stream_i_rst_vct_%s' % (main_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
input_stream_vct_shp = '%s/stream_i_rst_vct_%s/stream_i_rst_vct_%s.shp' % (
tmp_output_dir, str(ID), str(ID))
v.generalize(input='stream_i_rst_vct_%s' % str(ID), output='stream_i_rst_vct_gen_%s' % str(ID),
method='reduction', threshold='1000000000', overwrite=overwrite_mode, quiet=quiet_mode)
# v.out_ogr(input='stream_i_rst_vct_gen_%s'%str(ID), type="line", output='%s/stream_i_rst_vct_gen_%s'%(tmp_output_dir,str(ID)), format="ESRI_Shapefile", overwrite = overwrite_mode, quiet = quiet_mode)
# Buffer streams
r.buffer(input='stream_i_%s' % str(ID), output='stream_buff_i_%s' % str(ID),
distances='%s' % (str(buffer_distance_cells)), overwrite=overwrite_mode, quiet=quiet_mode)
# # First method clip over stream buffer center line boundary
# r.mapcalc("stream_buff_i_fc_%s=if(stream_buff_i_%s==1,1,null())"%(str(ID),str(ID)), overwrite = overwrite_mode, quiet = quiet_mode)
# r.mapcalc("stream_buff_sv_i_%s=if(isnull(stream_buff_i_fc_%s),null(),1)"%(str(ID),str(ID)), overwrite = overwrite_mode, quiet = quiet_mode)
# g.region(raster='stream_buff_sv_i_%s'%str(ID), quiet = quiet_mode)
# g.region(zoom='stream_buff_sv_i_%s'%str(ID), quiet = quiet_mode)
# Clip over stream buffer
r.mapcalc("stream_buff_sv_i_%s=if(isnull(stream_buff_i_%s),null(),1)" % (str(ID), str(ID)),
overwrite=overwrite_mode, quiet=quiet_mode)
g.region(raster='stream_buff_sv_i_%s' % str(ID), quiet=quiet_mode)
g.region(zoom='stream_buff_sv_i_%s' % str(ID), quiet=quiet_mode)
r.mask(raster='stream_buff_sv_i_%s' % str(ID))
# Clip DEM
r.mapcalc("dem_i_%s=raw_dem" % str(ID), overwrite=overwrite_mode, quiet=quiet_mode)
# r.out_gdal(input='dem_i_%s'%str(ID), output='%s/dem_i_%s.tif'%(tmp_output_dir,ID), createopt="COMPRESS=DEFLATE", overwrite = overwrite_mode, quiet = quiet_mode)
r.mask(flags='r')
# Extract points to process
v.to_points_new(input='stream_i_rst_vct_gen_%s' % str(ID),
output='stream_i_vect_start_point_%s' % str(ID),
use='start', overwrite=overwrite_mode, quiet=quiet_mode)
v.to_points_new(input='stream_i_rst_vct_%s' % str(ID), output='stream_i_vect_all_point_%s' % str(ID),
use='vertex', overwrite=overwrite_mode, quiet=quiet_mode)
v.to_points_new(input='stream_i_rst_vct_gen_%s' % str(ID),
output='stream_i_vect_end_point_%s' % str(ID),
use='end', overwrite=overwrite_mode, quiet=quiet_mode)
# Make mask start + end point
v.to_rast(input='stream_i_vect_start_point_%s' % str(ID),
output='stream_i_vect_start_point_rst_%s' % str(ID), type='point', use='attr',
attribute_column='value', overwrite=overwrite_mode, quiet=quiet_mode)
v.to_rast(input='stream_i_vect_end_point_%s' % str(ID),
output='stream_i_vect_end_point_rst_%s' % str(ID),
type='point', use='attr', attribute_column='value', overwrite=overwrite_mode,
quiet=quiet_mode)
r.mapcalc("start_point_mask_%s=if(!isnull(stream_i_vect_start_point_rst_%s),1,0)" % (str(ID), str(ID)),
overwrite=overwrite_mode, quiet=quiet_mode)
r.mapcalc("end_point_mask_%s=if(!isnull(stream_i_vect_end_point_rst_%s),1,0)" % (str(ID), str(ID)),
overwrite=overwrite_mode, quiet=quiet_mode)
r.mapcalc("startend_mask_%s=start_point_mask_%s+end_point_mask_%s" % (str(ID), str(ID), str(ID)),
overwrite=overwrite_mode, quiet=quiet_mode)
# v.out_ogr(input='stream_i_vect_start_point_%s'%str(ID), type="point", output='%s/stream_i_vect_start_point_%s'%(tmp_output_dir,str(ID)), format="ESRI_Shapefile", overwrite = overwrite_mode, quiet = quiet_mode)
# v.out_ogr(input='stream_i_vect_all_point_%s'%str(ID), type="point", output='%s/stream_i_vect_all_point_%s'%(tmp_output_dir,str(ID)), format="ESRI_Shapefile", overwrite = overwrite_mode, quiet = quiet_mode)
# v.out_ogr(input='stream_i_vect_end_point_%s'%str(ID), type="point", output='%s/stream_i_vect_end_point_%s'%(tmp_output_dir,str(ID)), format="ESRI_Shapefile", overwrite = overwrite_mode, quiet = quiet_mode)
r.mapcalc("start_point_elev_%s=if(!isnull(stream_i_vect_start_point_rst_%s),raw_dem,null())" % (
str(ID), str(ID)), overwrite=overwrite_mode, quiet=quiet_mode)
r.mapcalc(
"end_point_elev_%s=if(!isnull(stream_i_vect_end_point_rst_%s),raw_dem,null())" % (
str(ID), str(ID)),
overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='start_point_elev_%s' % str(ID),
output='%s/start_point_elev_%s.tif' % (tmp_output_dir, ID), createopt="COMPRESS=DEFLATE",
overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='end_point_elev_%s' % str(ID),
output='%s/end_point_elev_%s.tif' % (tmp_output_dir, ID), createopt="COMPRESS=DEFLATE",
overwrite=overwrite_mode, quiet=quiet_mode)
r.to_vect(input='start_point_elev_%s' % str(ID), output='start_point_elev_point_%s' % str(ID),
type='point', overwrite=overwrite_mode, quiet=quiet_mode)
r.to_vect(input='end_point_elev_%s' % str(ID), output='end_point_elev_point_%s' % str(ID),
type='point',
overwrite=overwrite_mode, quiet=quiet_mode)
v.out_ogr(input='start_point_elev_point_%s' % str(ID), type="point",
output='%s/start_point_elev_point_%s' % (tmp_output_dir, str(ID)),
format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
v.out_ogr(input='end_point_elev_point_%s' % str(ID), type="point",
output='%s/end_point_elev_point_%s' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
v.db_dropcolumn(map='stream_i_vect_start_point_%s' % str(ID), columns='value', quiet=quiet_mode)
v.db_dropcolumn(map='stream_i_vect_start_point_%s' % str(ID), columns='label', quiet=quiet_mode)
v.db_addcolumn(map='stream_i_vect_start_point_%s' % str(ID), columns="POS integer")
v.db_addcolumn(map='stream_i_vect_start_point_%s' % str(ID), columns="value double precision")
v.what_rast(map='stream_i_vect_start_point_%s' % str(ID), raster='raw_dem', column='value',
quiet=quiet_mode)
v.out_ogr(input='stream_i_vect_start_point_%s' % str(ID), type="point",
output='%s/stream_i_vect_start_point_v2_%s' % (tmp_output_dir, str(ID)),
format="ESRI_Shapefile", overwrite=overwrite_mode, quiet=quiet_mode)
stream_i_vect_start_point_shp = '%s/stream_i_vect_start_point_v2_%s/%s.shp' % (
tmp_output_dir, str(ID), 'stream_i_vect_start_point_%s' % str(ID))
stream_i_vect_start_point_shape = gpd.read_file(stream_i_vect_start_point_shp)
stream_i_vect_start_point_shape_ed = stream_i_vect_start_point_shape.copy()
stream_i_vect_start_point_shape_ed = stream_i_vect_start_point_shape_ed.assign(POS=1)
stream_i_vect_start_point_shape_ed = stream_i_vect_start_point_shape_ed.assign(cat=1)
value_tmp = stream_i_vect_start_point_shape_ed.loc[
stream_i_vect_start_point_shape_ed['POS'] == 1, 'value']
start_point_elevation = value_tmp.values[0]
stream_i_vect_start_point_shape_ed = stream_i_vect_start_point_shape_ed[
['cat', 'value', 'POS', 'geometry']]
stream_i_vect_start_point_shp_v2 = '%s/%s_v2.shp' % (
tmp_output_dir, 'stream_i_vect_start_point_%s' % str(ID))
stream_i_vect_start_point_shape_ed.to_file(driver='ESRI Shapefile',
filename=stream_i_vect_start_point_shp_v2)
del stream_i_vect_start_point_shape, stream_i_vect_start_point_shape_ed, value_tmp
v.db_dropcolumn(map='stream_i_vect_end_point_%s' % str(ID), columns='value', quiet=quiet_mode)
v.db_dropcolumn(map='stream_i_vect_end_point_%s' % str(ID), columns='label', quiet=quiet_mode)
v.db_addcolumn(map='stream_i_vect_end_point_%s' % str(ID), columns="POS integer")
v.db_addcolumn(map='stream_i_vect_end_point_%s' % str(ID), columns="value double precision")
v.what_rast(map='stream_i_vect_end_point_%s' % str(ID), raster='raw_dem', column='value',
quiet=quiet_mode)
v.out_ogr(input='stream_i_vect_end_point_%s' % str(ID), type="point",
output='%s/stream_i_vect_end_point_v2_%s' % (tmp_output_dir, str(ID)),
format="ESRI_Shapefile", overwrite=overwrite_mode, quiet=quiet_mode)
stream_i_vect_end_point_shp = '%s/stream_i_vect_end_point_v2_%s/%s.shp' % (
tmp_output_dir, str(ID), 'stream_i_vect_end_point_%s' % str(ID))
stream_i_vect_end_point_shape = gpd.read_file(stream_i_vect_end_point_shp)
stream_i_vect_end_point_shape_ed = stream_i_vect_end_point_shape.copy()
stream_i_vect_end_point_shape_ed = stream_i_vect_end_point_shape_ed.assign(POS=1)
stream_i_vect_end_point_shape_ed = stream_i_vect_end_point_shape_ed.assign(cat=1)
value_tmp = stream_i_vect_end_point_shape_ed.loc[
stream_i_vect_end_point_shape_ed['POS'] == 1, 'value']
end_point_elevation = value_tmp.values[0]
stream_i_vect_end_point_shape_ed = stream_i_vect_end_point_shape_ed[
['cat', 'value', 'POS', 'geometry']]
stream_i_vect_end_point_shp_v2 = '%s/%s_v2.shp' % (
tmp_output_dir, 'stream_i_vect_end_point_%s' % str(ID))
stream_i_vect_end_point_shape_ed.to_file(driver='ESRI Shapefile',
filename=stream_i_vect_end_point_shp_v2)
del stream_i_vect_end_point_shape, stream_i_vect_end_point_shape_ed, value_tmp
if float(start_point_elevation) >= float(end_point_elevation):
v.in_ogr(flags="o", input=stream_i_vect_start_point_shp_v2,
output='real_inlet_point_%s' % str(ID),
quiet=quiet_mode)
v.in_ogr(flags="o", input=stream_i_vect_end_point_shp_v2,
output='real_outlet_point_%s' % str(ID),
quiet=quiet_mode)
v.out_ogr(input='real_inlet_point_%s' % str(ID), type="point",
output='%s/real_inlet_point_%s' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
v.out_ogr(input='real_outlet_point_%s' % str(ID), type="point",
output='%s/real_outlet_point_%s' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
else:
v.in_ogr(flags="o", input=stream_i_vect_start_point_shp_v2,
output='real_outlet_point_%s' % str(ID),
quiet=quiet_mode)
v.in_ogr(flags="o", input=stream_i_vect_end_point_shp_v2,
output='real_inlet_point_%s' % str(ID),
quiet=quiet_mode)
v.out_ogr(input='real_inlet_point_%s' % str(ID), type="point",
output='%s/real_inlet_point_%s' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
v.out_ogr(input='real_outlet_point_%s' % str(ID), type="point",
output='%s/real_outlet_point_%s' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
# Create masks
v.to_rast(input='real_inlet_point_%s' % str(ID), output='inlet_mask_%s' % str(ID), type='point',
use='attr', attribute_column='POS', overwrite=overwrite_mode, quiet=quiet_mode)
v.to_rast(input='real_outlet_point_%s' % str(ID), output='outlet_mask_%s' % str(ID), type='point',
use='attr', attribute_column='POS', overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='inlet_mask_%s' % str(ID), output='%s/inlet_mask_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='outlet_mask_%s' % str(ID), output='%s/outlet_mask_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
r.mapcalc("stream_mask_%s=if(!isnull(stream_i_thinned_%s),0,null())" % (str(ID), str(ID)),
overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='stream_mask_%s' % str(ID), output='%s/stream_mask_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
r.patch(input='inlet_mask_%s,outlet_mask_%s,stream_mask_%s' % (str(ID), str(ID), str(ID)),
output='inoutlet_mask_%s' % str(ID), overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='inoutlet_mask_%s' % str(ID),
output='%s/inoutlet_mask_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
r.mapcalc("stream_i_thinned_elev_rst_%s=if(stream_i_thinned_%s==%s,raw_dem,null())" % (
str(ID), str(ID), str(ID)), overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='stream_i_thinned_elev_rst_%s' % str(ID),
output='%s/stream_i_thinned_elev_rst_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
# Extract profile along stream (elevation VS progressive distance from inlet)
r.cost(input='stream_i_thinned_%s' % str(ID), output='progressive_%s' % str(ID),
start_raster='inlet_mask_%s' % str(ID), overwrite=overwrite_mode, quiet=quiet_mode)
r.out_gdal(input='progressive_%s' % str(ID), output='%s/progressive_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
# Calculate statistics
progressive_i_stats = grass.parse_command('r.univar', map='progressive_%s' % str(ID), flags='g')
progressive_i_count = int(progressive_i_stats['n']) # To verify how to get non-null cells
progressive_i_min = float(progressive_i_stats['min'])
progressive_i_max = float(progressive_i_stats['max'])
# Calculate standardized flow_acc
r.mapcalc("progressive_adim_%s=(progressive_%s-%s)/(%s-%s)" % (
str(ID), str(ID), str(progressive_i_min), str(progressive_i_max), str(progressive_i_min)),
overwrite=overwrite_mode, quiet=quiet_mode)
# Multiply flow_acc_i_adim by large number to avoid having problems reading small values E^x
r.mapcalc("progressive_adim_%s=progressive_adim_%s*1000" % (str(ID), str(ID)),
overwrite=overwrite_mode,
quiet=quiet_mode)
r.out_gdal(input='progressive_adim_%s' % str(ID),
output='%s/progressive_adim_%s.tif' % (tmp_output_dir, ID), createopt="COMPRESS=DEFLATE",
overwrite=overwrite_mode, quiet=quiet_mode)
r.mapcalc("progressive_adim_no_inoutlet_%s=if(inoutlet_mask_%s==0,progressive_adim_%s,null())" % (
str(ID), str(ID), str(ID)), overwrite=overwrite_mode, quiet=quiet_mode)
# Mask out zero values
r.mapcalc("inlet_mask_%s=if(inlet_mask_%s==1,1,null())" % (str(ID), str(ID)),
overwrite=overwrite_mode,
quiet=quiet_mode)
r.mapcalc("outlet_mask_%s=if(outlet_mask_%s==1,1,null())" % (str(ID), str(ID)),
overwrite=overwrite_mode, quiet=quiet_mode)
# Create raster inlet and outlet position
r.mapcalc("inlet_pos_%s=inlet_mask_%s*0" % (str(ID), str(ID)), overwrite=overwrite_mode,
quiet=quiet_mode)
r.mapcalc("outlet_pos_%s=outlet_mask_%s*(%s-1)" % (str(ID), str(ID), progressive_i_count),
overwrite=overwrite_mode, quiet=quiet_mode)
# Get outlet and inlet elevation
r.mapcalc("inlet_elev_%s=inlet_mask_%s*raw_dem" % (str(ID), str(ID)), overwrite=overwrite_mode,
quiet=quiet_mode)
r.out_gdal(input='inlet_elev_%s' % str(ID), output='%s/inlet_elev_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
r.mapcalc("outlet_elev_%s=outlet_mask_%s*raw_dem" % (str(ID), str(ID)), overwrite=overwrite_mode,
quiet=quiet_mode)
r.out_gdal(input='outlet_elev_%s' % str(ID), output='%s/outlet_elev_%s.tif' % (tmp_output_dir, ID),
createopt="COMPRESS=DEFLATE", overwrite=overwrite_mode, quiet=quiet_mode)
# Convert raster to point vector
r.to_vect(input='inlet_elev_%s' % str(ID), output='inlet_point_%s' % str(ID), type='point',
overwrite=overwrite_mode, quiet=quiet_mode)
v.out_ogr(input='inlet_point_%s' % str(ID), type="point",
output='%s/inlet_elev_vect_%s' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
inlet_point_shp = '%s/inlet_elev_vect_%s/inlet_point_%s.shp' % (tmp_output_dir, str(ID), str(ID))
# Replace standard ID with the position one
v.in_ogr(input=inlet_point_shp, output='inlet_point_%s_v2' % str(ID), quiet=quiet_mode)
v.what_rast(map='inlet_point_%s_v2' % str(ID), raster='inlet_pos_%s' % str(ID), column='cat_',
quiet=quiet_mode)
v.db_renamecolum(map='inlet_point_%s_v2' % str(ID), column=('cat_', 'POS'), quiet=quiet_mode)
v.out_ogr(input='inlet_point_%s_v2' % str(ID), type="point",
output='%s/inlet_elev_vect_%s_v2' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
inlet_point_shp_v2 = '%s/inlet_elev_vect_%s_v2/inlet_point_%s_v2.shp' % (
tmp_output_dir, str(ID), str(ID))
# Convert raster to point vector
r.to_vect(input='outlet_elev_%s' % str(ID), output='outlet_point_%s' % str(ID), type='point',
overwrite=overwrite_mode, quiet=quiet_mode)
v.out_ogr(input='outlet_point_%s' % str(ID), type="point",
output='%s/outlet_elev_vect_%s' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
outlet_point_shp = '%s/outlet_elev_vect_%s/outlet_point_%s.shp' % (tmp_output_dir, str(ID), str(ID))
# Replace standard ID with the position one
v.in_ogr(flags="o", input=outlet_point_shp, output='outlet_point_%s_v2' % str(ID), quiet=quiet_mode)
v.what_rast(map='outlet_point_%s_v2' % str(ID), raster='outlet_pos_%s' % str(ID), column='cat_',
quiet=quiet_mode)
v.db_renamecolum(map='outlet_point_%s_v2' % str(ID), column=('cat_', 'POS'), quiet=quiet_mode)
v.out_ogr(input='outlet_point_%s_v2' % str(ID), type="point",
output='%s/outlet_elev_vect_%s_v2' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
outlet_point_shp_v2 = '%s/outlet_elev_vect_%s_v2/outlet_point_%s_v2.shp' % (
tmp_output_dir, str(ID), str(ID))
# Convert raster to point vector
r.to_vect(input='progressive_adim_no_inoutlet_%s' % str(ID), output='extra_points_%s' % str(ID),
type='point', overwrite=overwrite_mode, quiet=quiet_mode)
v.out_ogr(input='extra_points_%s' % str(ID), type="point",
output='%s/extra_vect_%s' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
extra_points_shp = '%s/extra_vect_%s/extra_points_%s.shp' % (tmp_output_dir, str(ID), str(ID))
# Sort values ascending and export sorted shapefile with new ID. ID is the cell position in downstream direction from 1 to non null cells (withouth inlet and outlet)
extra_points_shp_ordered = '%s/extra_vect_orderd_%s.shp' % (tmp_output_dir, str(ID))
shape = gpd.read_file(extra_points_shp)
shape = shape.assign(POS=0)
shape_sorted = shape.iloc[shape['value'].sort_values(ascending=[True]).index.values]
all_values = shape_sorted['value'].values
count = 0
for value_i in all_values:
count += 1
shape_sorted.loc[shape_sorted['value'] == value_i, 'POS'] = count
shape_sorted = shape_sorted[['cat', 'value', 'POS', 'geometry']]
shape_sorted.to_file(driver='ESRI Shapefile', filename=extra_points_shp_ordered)
v.in_ogr(flags="o", input=extra_points_shp_ordered, output='stream_points_ordered_%s' % str(ID),
quiet=quiet_mode)
# Delete cat_ field
v.db_dropcolumn(map='stream_points_ordered_%s' % str(ID), columns='cat_', quiet=quiet_mode)
# Extract elevation from raster at point location (replace values into "value" Field)
v.what_rast(map='stream_points_ordered_%s' % str(ID), raster='dem_i_%s' % str(ID), column='value',
quiet=quiet_mode)
v.out_ogr(input='stream_points_ordered_%s' % str(ID), type="point",
output='%s/stream_elev_vect_%s' % (tmp_output_dir, str(ID)), format="ESRI_Shapefile",
overwrite=overwrite_mode, quiet=quiet_mode)
stream_elev_points_shp = '%s/stream_elev_vect_%s/stream_points_ordered_%s.shp' % (
tmp_output_dir, str(ID), str(ID))
# Extract profile array
shape_str_elev = gpd.read_file(stream_elev_points_shp)
shape_str_elev_sorted = shape_str_elev.iloc[
shape_str_elev['POS'].sort_values(ascending=[True]).index.values]
str_elev_x = shape_str_elev_sorted['POS'].values
str_elev_z = shape_str_elev_sorted['value'].values
str_elev_geom = shape_str_elev_sorted['geometry'].values
del shape_str_elev
str_elev_x_lst = str_elev_x.tolist()
str_elev_z_lst = str_elev_z.tolist()
shape_inlet_elev = gpd.read_file(inlet_point_shp_v2)
inlet_elev_x = shape_inlet_elev['POS'].values
inlet_elev_z = shape_inlet_elev['value'].values
inlet_elev_geom = shape_inlet_elev['geometry'].values
del shape_inlet_elev
inlet_elev_x_lst = inlet_elev_x.tolist()
inlet_elev_z_lst = inlet_elev_z.tolist()
shape_outlet_elev = gpd.read_file(outlet_point_shp_v2)
outlet_elev_x = shape_outlet_elev['POS'].values
outlet_elev_z = shape_outlet_elev['value'].values
outlet_elev_geom = shape_outlet_elev['geometry'].values
del shape_outlet_elev
outlet_elev_x_lst = outlet_elev_x.tolist()
outlet_elev_z_lst = outlet_elev_z.tolist()
all_stream_elev_x = np.concatenate((inlet_elev_x, str_elev_x, outlet_elev_x))
all_stream_elev_z = np.concatenate((inlet_elev_z, str_elev_z, outlet_elev_z))
all_stream_elev_geom = np.concatenate((inlet_elev_geom, str_elev_geom, outlet_elev_geom))
all_stream_elev_x_lst = all_stream_elev_x.tolist()
all_stream_elev_z_lst = all_stream_elev_z.tolist()
str_elev_x_m = all_stream_elev_x + 1
str_elev_x_m = str_elev_x_m[:-2]
str_elev_z_m = all_stream_elev_z[:-2]
str_elev_x_m_lst = str_elev_x_m.tolist()
str_elev_z_m_lst = str_elev_z_m.tolist()
str_elev_x_p = all_stream_elev_x - 1
str_elev_x_p = str_elev_x_p[2:]
str_elev_z_p = all_stream_elev_z[2:]
str_elev_x_p_lst = str_elev_x_p.tolist()
str_elev_z_p_lst = str_elev_z_p.tolist()
# Compute z-z_m and z_p-z
delta_z_m = str_elev_z - str_elev_z_m
delta_z_p = str_elev_z_p - str_elev_z
delta_z_m_lst = delta_z_m.tolist()
delta_z_p_lst = delta_z_p.tolist()
# Compute |(dz_p-dz_m)*n_pixels|
Dz_2 = abs((delta_z_p - delta_z_m) * 2)
Dz_2_lst = Dz_2.tolist()
# Compute average DZ
avg_Dz = (inlet_elev_z[0] - outlet_elev_z[0]) / (progressive_i_count - 1)
A = np.vstack((str_elev_x, str_elev_z, Dz_2)).T
avg_Dz = avg_Dz / filtering_magnitude
F = A[A[:, 2] < avg_Dz]
X_filt = F[:, 0]
Z_filt = F[:, 1]
X_filt_lst = X_filt.tolist()
Z_filt_lst = Z_filt.tolist()
all_stream_filt_elev_x = np.concatenate((inlet_elev_x, X_filt, outlet_elev_x))
all_stream_filt_elev_z = np.concatenate((inlet_elev_z, Z_filt, outlet_elev_z))
all_stream_filt_elev_x_lst = all_stream_filt_elev_x.tolist()
all_stream_filt_elev_z_lst = all_stream_filt_elev_z.tolist()
window_length = progressive_i_count / 100.0
odd_window_length_int = int(np.ceil(window_length / 2.) * 2 + 1)
odd_window_length_int = 3 * odd_window_length_int
# logging.info('window_length')
# logging.info(window_length)
# logging.info('progressive_i_count')
# logging.info(progressive_i_count)
# logging.info('odd_window_length_int')
# logging.info(odd_window_length_int)
f = interpolate.interp1d(all_stream_filt_elev_x_lst, all_stream_filt_elev_z_lst)
str_elev_x_interp_lst = np.arange(0, progressive_i_count, 1)
str_elev_z_interp_lst = f(str_elev_x_interp_lst)
str_elev_x_interp = np.array(str_elev_x_interp_lst)
str_elev_z_interp = np.array(str_elev_z_interp_lst)
str_elev_z_interp_sm_lst = savgol_filter(str_elev_z_interp_lst, odd_window_length_int, 3)
str_elev_z_interp_sm = np.array(str_elev_z_interp_sm_lst)
str_elev_z_interp_adim = (
(all_stream_filt_elev_z - outlet_elev_z[0]) / (inlet_elev_z[0] - outlet_elev_z[0]))
if flat_burning_mode_flag == False:
str_elev_z_burned = (all_stream_filt_elev_z - ((1 - str_elev_z_interp_adim) * burning_depth))
str_elev_z_burned_lst = str_elev_z_burned.tolist()
else:
str_elev_z_burned = (all_stream_filt_elev_z - burning_depth)
str_elev_z_burned_lst = str_elev_z_burned.tolist()
f = interpolate.interp1d(all_stream_filt_elev_x_lst, str_elev_z_burned_lst)
str_elev_x_burn_interp_lst = np.arange(0, progressive_i_count, 1)
str_elev_z_burn_interp_lst = f(str_elev_x_burn_interp_lst)
str_elev_x_burn_interp = np.array(str_elev_x_burn_interp_lst)
str_elev_z_burn_interp = np.array(str_elev_z_burn_interp_lst)
str_elev_z_burn_interp_sm_lst = savgol_filter(str_elev_z_burn_interp, odd_window_length_int, 3)
str_elev_z_burn_interp_sm = np.array(str_elev_z_burn_interp_sm_lst)
out_csv_file = '%s/river_profile_%s_orig.csv' % (tmp_output_dir, str(ID))
with open(out_csv_file, "w") as outfile:
entry = 'POS,Z'
outfile.write(entry)
outfile.write("\n")
with open(out_csv_file, "a") as outfile:
for i in range(len(all_stream_elev_x_lst)):
entry = '%s,%s' % (str(all_stream_elev_x_lst[i]), str(all_stream_elev_z_lst[i]))
outfile.write(entry)
outfile.write("\n")
out_csv_file_fil = '%s/river_profile_%s_filtered_%s_%s.csv' % (
tmp_output_dir, str(ID), str(buffer_distance_cells), str(filtering_magnitude))
with open(out_csv_file_fil, "w") as outfile:
entry = 'POS_INT,Z_INT'
outfile.write(entry)
outfile.write("\n")
with open(out_csv_file_fil, "a") as outfile:
for i in range(len(str_elev_x_interp_lst)):
entry = '%s,%s' % (str(str_elev_x_interp_lst[i]), str(str_elev_z_interp_lst[i]))
outfile.write(entry)
outfile.write("\n")
out_csv_file_fil = '%s/river_profile_%s_filtered_sm_%s_%s.csv' % (
tmp_output_dir, str(ID), str(buffer_distance_cells), str(filtering_magnitude))
with open(out_csv_file_fil, "w") as outfile:
entry = 'POS_INT_SM,Z_INT_SM'
outfile.write(entry)
outfile.write("\n")
with open(out_csv_file_fil, "a") as outfile:
for i in range(len(str_elev_x_interp_lst)):
entry = '%s,%s' % (str(str_elev_x_interp_lst[i]), str(str_elev_z_interp_sm_lst[i]))
outfile.write(entry)
outfile.write("\n")
out_csv_file_bur = '%s/river_profile_%s_burned_%s_%s_%s.csv' % (
main_output_dir, str(ID), str(buffer_distance_cells), str(filtering_magnitude), str(burning_depth))
with open(out_csv_file_bur, "w") as outfile:
entry = 'POS_BUR,Z_BUR'
outfile.write(entry)
outfile.write("\n")
with open(out_csv_file_bur, "a") as outfile:
for i in range(len(str_elev_x_burn_interp_lst)):
entry = '%s,%s' % (str(str_elev_x_burn_interp_lst[i]), str(str_elev_z_burn_interp_lst[i]))
outfile.write(entry)
outfile.write("\n")
out_csv_file_bur = '%s/river_profile_%s_burned_sm_%s_%s_%s.csv' % (
tmp_output_dir, str(ID), str(buffer_distance_cells), str(filtering_magnitude), str(burning_depth))
with open(out_csv_file_bur, "w") as outfile:
entry = 'POS_BUR_SM,Z_BUR_SM'
outfile.write(entry)
outfile.write("\n")
with open(out_csv_file_bur, "a") as outfile:
for i in range(len(str_elev_x_burn_interp_lst)):
entry = '%s,%s' % (
str(str_elev_x_burn_interp_lst[i]), str(str_elev_z_burn_interp_sm_lst[i]))
outfile.write(entry)
outfile.write("\n")
# Make a river 2D graph
plt.plot(all_stream_elev_x_lst, all_stream_elev_z_lst, linewidth=0.3, label='Raw DEM',
color='black')
plt.plot(str_elev_x_interp_lst, str_elev_z_interp_lst, linewidth=0.5, label='Filtered',
color='blue')
plt.plot(str_elev_x_burn_interp_lst, str_elev_z_interp_sm_lst, linewidth=0.3, linestyle='dashed',
label='Filtered sm', color='blue')
plt.plot(str_elev_x_burn_interp_lst, str_elev_z_burn_interp_lst, linewidth=0.5, label='Burned',
color='brown')
plt.plot(str_elev_x_burn_interp_lst, str_elev_z_burn_interp_sm_lst, linewidth=0.3,
linestyle='dashed',
label='Burned sm', color='brown')
plt.xlabel("Stream vertex no.")
plt.ylabel("Elevation (m)")
plt.title('Stream no. %s' % (str(ID)))
plt.legend()
plt.savefig('%s/river_profile_%s_%s_%s.png' % (
main_output_dir, str(ID), str(buffer_distance_cells), str(filtering_magnitude)))
plt.close()
# Import array and recreate shp
final_points_shp = '%s/final_vect_%s.shp' % (tmp_output_dir, str(ID))
str_elev_z_burn_interpm = str_elev_z_burn_interp[:-1]
str_elev_z_burn_interpmp = str_elev_z_burn_interpm[1:]
shape_str_elev = gpd.read_file(stream_elev_points_shp)
shape_str_elev_sorted = shape_str_elev.iloc[
shape_str_elev['POS'].sort_values(ascending=[True]).index.values]
all_pos = shape_str_elev_sorted['POS'].values
count = 0
for pos_i in all_pos:
shape_str_elev_sorted.loc[shape_str_elev_sorted['POS'] == pos_i, 'value'] = \
str_elev_z_burn_interpmp[count]
count += 1
shape_str_elev_sorted = shape_str_elev_sorted[['cat', 'value', 'POS', 'geometry']]
shape_str_elev_sorted.to_file(driver='ESRI Shapefile', filename=final_points_shp)
v.in_ogr(flags="o", input=final_points_shp, output='final_points_vector_%s' % str(ID),
quiet=quiet_mode)
r.mapcalc("outlet_elev_burned_%s=outlet_elev_%s-%s" % (str(ID), str(ID), str(burning_depth)),
overwrite=overwrite_mode, quiet=quiet_mode)
v.to_rast(input='final_points_vector_%s' % str(ID), output='final_points_rast_%s' % str(ID),
type='point', use='attr', attribute_column='value', overwrite=overwrite_mode,
quiet=quiet_mode)